# Abundance of Euphausia pacifica over Time
## # A tibble: 12 × 2
## ID_Microscopy n
## <chr> <int>
## 1 Euphausia pacifica 21182
## 2 Nematoscelis difficilis 20967
## 3 Thysanoessa gregaria 12294
## 4 Nyctiphanes simplex 10117
## 5 Stylocheiron longicorne 7717
## 6 Euphausia recurva 6338
## 7 Euphausia gibboides 4430
## 8 Stylocheiron affine 4392
## 9 Thysanoessa spinifera 3579
## 10 Stylocheiron maximum 2567
## 11 Euphausia eximia 1311
## 12 Nematobrachion flexipes 1179
## Warning: There was 1 warning in `filter()`.
## ℹ In argument: `!is.na(year)`.
## Caused by warning in `is.na()`:
## ! is.na() applied to non-(list or vector) of type 'closure'
## Warning: The dot-dot notation (`..eq.label..`) was deprecated in ggplot2 3.4.0.
## ℹ Please use `after_stat(eq.label)` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning: Removed 792 rows containing non-finite values (`stat_smooth()`).
## Warning: Removed 792 rows containing non-finite values (`stat_poly_eq()`).
## Removed 792 rows containing non-finite values (`stat_poly_eq()`).
## Warning: Removed 792 rows containing missing values (`geom_point()`).
## Warning: Removed 792 rows containing non-finite values (`stat_smooth()`).
## Warning: Removed 792 rows containing non-finite values (`stat_poly_eq()`).
## Warning: Removed 792 rows containing missing values (`geom_point()`).
# Abundance Temp + O2 Envelope
## Warning: Removed 134 rows containing missing values (`geom_point()`).
## Warning: Removed 134 rows containing missing values (`geom_point()`).
## Warning: Removed 57 rows containing missing values (`geom_point()`).
# Site - Binomial vs. SST
## Warning in checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv, :
## Model failed to converge with max|grad| = 0.00455353 (tol = 0.002, component 1)
## Generalized linear mixed model fit by maximum likelihood (Laplace
## Approximation) [glmerMod]
## Family: binomial ( logit )
## Formula: PA ~ (1 | ID_Microscopy) + mean_temp * mean_O2ml_L
## Data: pa_adult_data
##
## AIC BIC logLik deviance df.resid
## 18626.3 18666.5 -9308.2 18616.3 22711
##
## Scaled residuals:
## Min 1Q Median 3Q Max
## -1.2370 -0.5766 -0.2175 -0.0823 12.9409
##
## Random effects:
## Groups Name Variance Std.Dev.
## ID_Microscopy (Intercept) 3.147 1.774
## Number of obs: 22716, groups: ID_Microscopy, 12
##
## Fixed effects:
## Estimate Std. Error z value Pr(>|z|)
## (Intercept) -11.19166 1.30134 -8.600 < 2e-16 ***
## mean_temp 0.82952 0.10671 7.774 7.63e-15 ***
## mean_O2ml_L 1.89486 0.25002 7.579 3.49e-14 ***
## mean_temp:mean_O2ml_L -0.17096 0.02177 -7.851 4.12e-15 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Correlation of Fixed Effects:
## (Intr) mn_tmp m_O2_L
## mean_temp -0.912
## mean_O2ml_L -0.902 0.959
## mn_tm:_O2_L 0.908 -0.983 -0.990
## optimizer (Nelder_Mead) convergence code: 0 (OK)
## Model failed to converge with max|grad| = 0.00455353 (tol = 0.002, component 1)
Example Euphausia pacifica
## Warning: Using `size` aesthetic for lines was deprecated in ggplot2 3.4.0.
## ℹ Please use `linewidth` instead.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.
## Warning in eval(family$initialize): non-integer #successes in a binomial glm!
## Warning: `fitted_draws` and `add_fitted_draws` are deprecated as their names were confusing.
## - Use [add_]epred_draws() to get the expectation of the posterior predictive.
## - Use [add_]linpred_draws() to get the distribution of the linear predictor.
## - For example, you used [add_]fitted_draws(..., scale = "response"), which
## means you most likely want [add_]epred_draws(...).
## NOTE: When updating to the new functions, note that the `model` parameter is now
## named `object` and the `n` parameter is now named `ndraws`.